implemente the threading option for minimap2

Author: cokelaer

README.rst

@@ -76,6 +76,7 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+0.8.13    * add the thread option in minimap2 case
 0.8.12    * factorise multiqc rule
 0.8.11    * Implemente the --from-project option and new framework
           * custom HTMrLl report

sequana_pipelines/mapper/config.yaml

@@ -29,6 +29,7 @@ bwa_mem_mapping:
 
 minimap2:
     options: ''
+    threads: 4
 
 bowtie2_mapping_ref:
     options:

sequana_pipelines/mapper/mapper.rules

@@ -80,12 +80,13 @@ elif config['general']['mapper'] == "minimap2":
     rule minimap2:
         input: __data__input
         output: __minimap2__output
+        threads: config["minimap2"]["threads"]
         params:
             reference=config['general']['reference_file'],
             options=config['minimap2']['options']
         shell:
             """
-            minimap2 {params.reference} {input} {params.options} -a | samtools view -b | bamtools sort -in - -out {output}
+            minimap2 -t {threads} {params.reference} {input} {params.options} -a | samtools view -b | bamtools sort -in - -out {output}
             """
     __bamtools_stats__input = __minimap2__output
 elif config['general']['mapper'] == "bowtie2":

sequana_pipelines/mapper/multiqc_config.yaml

@@ -131,6 +131,6 @@ table_columns_visible:
     FastQC:
         percent_fails: False
         total_sequences: True
-        percent_duplicates: False
+        percent_duplicates: True
         percent_gc: True
         avg_sequence_length: True

sequana_pipelines/mapper/schema.yaml

@@ -51,6 +51,9 @@ mapping:
         mapping:
             "options":
                 type: str
+            "threads": 
+                type: int
+                range: { min: 1 }
 
     "sequana_coverage":
         type: map

setup.py

@@ -7,7 +7,7 @@
 
 _MAJOR               = 0
 _MINOR               = 8
-_MICRO               = 12
+_MICRO               = 13
 version              = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
 release              = '%d.%d' % (_MAJOR, _MINOR)